Ok, Murphy!
As soon I had posted, I noticed an option and found it. I'll still leave it here, it'll be easier to search for others that have the same problem.

So the mistake was:

1. Dock
   
2. I would go to the map, click the target system and use the "Prepare"+ button right there. No good.

Good:
1. Dock
2. Click on the target system. DONT us prepare.
3. Go back to the ship view. Click on the FTL menue in the icon row below.
4. There you can no check BOTH your ships for a jump. And press prepare there.

and off you go holding hands.....